rs12244977

Variant names:

• chr10-57332922-T-G
• rs12244977
• XR_001747453.1:n.484-10246A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001747453.1(LOC105378313):​n.484-10246A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,942 control chromosomes in the GnomAD database, including 3,702 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (3702 hom., cov: 31)
• Consequence: LOC105378313 XR_001747453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 4 publications found

Genes affected

LOC105378313 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378313	XR_001747453.1	n.484-10246A>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23875 AN: 151824 Hom.: 3691 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0453

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.0859

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.135

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.158 AC: 23940 AN: 151942 Hom.: 3702 Cov.: 31 AF XY: 0.158 AC XY: 11735 AN XY: 74270

African (AFR) AF: 0.396 AC: 16365 AN: 41372

American (AMR) AF: 0.207 AC: 3154 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0453 AC: 157 AN: 3468

East Asian (EAS) AF: 0.0938 AC: 483 AN: 5148

South Asian (SAS) AF: 0.0851 AC: 410 AN: 4818

European-Finnish (FIN) AF: 0.0292 AC: 309 AN: 10598

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.0401 AC: 2723 AN: 67980

Other (OTH) AF: 0.135 AC: 286 AN: 2114

Alfa AF: 0.0731 Hom.: 564

Bravo AF: 0.182

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.36
PhyloP100		-0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12244977; hg19: chr10-59092682;